Inspecting electron density maps: Difference between revisions
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(copied & pasted from email from oliv) |
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Download coordinates and structure factor file | Download coordinates and structure factor file | ||
# Download 3ODU.pdb | # Download 3ODU.pdb | ||
# Download 3odu-sf.cif | # Download 3odu-sf.cif [http://eds.bmc.uu.se/] | ||
Open coot | Open coot | ||
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*B) You can center the view by clicking on the atom of interest with the middle mouse button | *B) You can center the view by clicking on the atom of interest with the middle mouse button | ||
*C) Zoom with right mouse button | *C) Zoom with right mouse button | ||
Pymol instructions: | |||
Here are the pymol lines to load the maps (for A2A in this case, | |||
sigmalevel 1 using second line). The map here is in ccp4 format, but | |||
other will work too (but depends on your pymol version): | |||
load 3eml.ccp4,map1 | |||
isomesh msh1,map1,1 | |||
load 3eml.pdb | |||
[[Category: Tutorials]] | |||
Latest revision as of 20:27, 8 October 2012
Download coordinates and structure factor file
- Download 3ODU.pdb
- Download 3odu-sf.cif [1]
Open coot
/raid3/software/coot/coot-0.6-Linux-x86_64/bin/coot &
Load molecule and map
- File-> Open Coordinates -> 3ODU.pdb
- File-> Open MTZ, mmCIF, fcf or phs.. -> 3odu-sf.cif
- Draw -> Go to atom > Chain A, residue 1500 -> Apply
Coot ABC
- A) Rotate with left mouse button
- B) You can center the view by clicking on the atom of interest with the middle mouse button
- C) Zoom with right mouse button
Pymol instructions: Here are the pymol lines to load the maps (for A2A in this case, sigmalevel 1 using second line). The map here is in ccp4 format, but other will work too (but depends on your pymol version):
load 3eml.ccp4,map1 isomesh msh1,map1,1 load 3eml.pdb